DFT studies on helix formation in N-acetyl-(L-alanyl)n-N′-methylamide for n=1-20
DFT studies on helix formation in N-acetyl-(L-alanyl)n-N′-methylamide for n=1-20
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DOI：
10.1016/s0301-0104(00)00100-2
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发表时间：
2000-05-15
期刊：
影响因子：
2.3
通讯作者：
Suhai, S
中科院分区：
文献类型：
--
作者：
Elstner, M;Jalkanen, KJ;Suhai, S
我们比较了一组封闭肽模型N-乙酰基-（L-丙氨酰）（n）-N '-甲基酰胺（n = 1-20）的重要二级结构元件3.6（13）螺旋、3（10）螺旋和C-5（ext）结构的几何形状和相对能量。我们采用B3 LYP/6- 31 G * 水平上的全密度泛函理论（DFT）计算（对于多肽上的Toll残基）、自洽电荷密度泛函紧密结合（SCC-DFTB）和半经验AM 1方法。发现3.6（13）和3（10）结构一般不是固有稳定的。它们的稳定性取决于肽长度、其他结构基序和水或膜环境。对于少于8个残基的短肽，3.6（13）螺旋松弛成3（10）结构。对于较长的肽，3.6（13）在链的中间是稳定的，而末端呈现3（10）构象，在C-末端另外形成β II型转角。用最近发展的SCC-DFTB方法计算的相对能量和结构与B3 LYP密度泛函计算的结果非常一致。因此，我们使用SCC-DFTB方法来观察N-乙酰基-（L-丙氨酰基）（n）-N '-甲基酰胺（n = 11、14、17和20）中的螺旋形成。在SCC-DFTB势能面上，我们发现对于所有肽大小，3（10）螺旋比3.6（13）螺旋更稳定。然而，溶液的影响可能会改变这种情况，并有利于3.6（13）基序。(C)2000 Elsevier Science B. V.保留所有权利。
We compare the geometries and relative energies of important secondary structural elements, the 3.6(13) helix, 3(10) helix and C-5(ext) structures, for a set of blocked peptide models, N-acetyl-(L-alanyl)(n)-N'-methylamide, for n = 1-20. We use full density-functional theory (DFT) calculations at the B3LYP/6-31G* level (for peptides up toll residues), the self-consistent-charge density-functional tight binding (SCC-DFTB) and the semiempirical AM1 method. The 3.6(13) and 3(10) structures are found to be not inherently stable in general. Their stability is dependent on peptide length, other structural motifs and aqueous or membrane environments. For short peptides with less than eight residues, the 3.6(13) helix relaxes into the 3(10) structure. For longer peptides, the 3.6(13) is Stable in the middle of the chain, while the ends assume 3(10) conformations, at the C-terminus additionally a beta II type turn is formed. The relative energies and structures calculated with the recently developed SCC-DFTB method are in very good agreement with the results from the B3LYP density-functional calculations. Therefore, we use the SCC-DFTB method to look at helix formation in N-acetyl-(L-alanyl)(n)-N'-methylamide for n = 11, 14, 17 and 20. On the SCC-DFTB potential energy surface, we find the 3(10) helix to be more stable than the 3.6(13) helix for all peptide sizes. However, the effects of solution might change this picture and favor the 3.6(13) motif. (C) 2000 Elsevier Science B.V. All rights reserved.